3WWQ

Crystal structure of FAAP20 UBZ domain in complex with Lys63-linked diubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report



Literature

Structural Basis for Ubiquitin Recognition by Ubiquitin-Binding Zinc Finger of FAAP20

Toma, A.Takahashi, T.S.Sato, Y.Yamagata, A.Goto-Ito, S.Nakada, S.Fukuto, A.Horikoshi, Y.Tashiro, S.Fukai, S.

(2015) PLoS One 10: e0120887-e0120887

  • DOI: 10.1371/journal.pone.0120887
  • Primary Citation of Related Structures:  
    3WWQ

  • PubMed Abstract: 
  • Several ubiquitin-binding zinc fingers (UBZs) have been reported to preferentially bind K63-linked ubiquitin chains. In particular, the UBZ domain of FAAP20 (FAAP20-UBZ), a member of the Fanconi anemia core complex, seems to recognize K63-linked ubiq ...

    Several ubiquitin-binding zinc fingers (UBZs) have been reported to preferentially bind K63-linked ubiquitin chains. In particular, the UBZ domain of FAAP20 (FAAP20-UBZ), a member of the Fanconi anemia core complex, seems to recognize K63-linked ubiquitin chains, in order to recruit the complex to DNA interstrand crosslinks and mediate DNA repair. By contrast, it is reported that the attachment of a single ubiquitin to Rev1, a translesion DNA polymerase, increases binding of Rev1 to FAAP20. To clarify the specificity of FAAP20-UBZ, we determined the crystal structure of FAAP20-UBZ in complex with K63-linked diubiquitin at 1.9 Å resolution. In this structure, FAAP20-UBZ interacts only with one of the two ubiquitin moieties. Consistently, binding assays using surface plasmon resonance spectrometry showed that FAAP20-UBZ binds ubiquitin and M1-, K48- and K63-linked diubiquitin chains with similar affinities. Residues in the vicinity of Ala168 within the α-helix and the C-terminal Trp180 interact with the canonical Ile44-centered hydrophobic patch of ubiquitin. Asp164 within the α-helix and the C-terminal loop mediate a hydrogen bond network, which reinforces ubiquitin-binding of FAAP20-UBZ. Mutations of the ubiquitin-interacting residues disrupted binding to ubiquitin in vitro and abolished the accumulation of FAAP20 to DNA damage sites in vivo. Finally, structural comparison among FAAP20-UBZ, WRNIP1-UBZ and RAD18-UBZ revealed distinct modes of ubiquitin binding. UBZ family proteins could be divided into at least three classes, according to their ubiquitin-binding modes.


    Organizational Affiliation

    Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinADGJ76Mus musculusMutation(s): 1 
Gene Names: Ubc
Find proteins for P0CG50 (Mus musculus)
Explore P0CG50 
Go to UniProtKB:  P0CG50
NIH Common Fund Data Resources
IMPC  MGI:98889
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinBEHK77Mus musculusMutation(s): 0 
Gene Names: Ubc
Find proteins for P0CG50 (Mus musculus)
Explore P0CG50 
Go to UniProtKB:  P0CG50
NIH Common Fund Data Resources
IMPC  MGI:98889
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fanconi anemia-associated protein of 20 kDaCFIL44Homo sapiensMutation(s): 0 
Gene Names: C1orf86FAAP20FP7162
Find proteins for Q6NZ36 (Homo sapiens)
Explore Q6NZ36 
Go to UniProtKB:  Q6NZ36
NIH Common Fund Data Resources
PHAROS  Q6NZ36
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
C, F, I, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.767α = 90
b = 45.85β = 98.06
c = 172.9γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2014-06-23 
  • Released Date: 2015-05-13 
  • Deposition Author(s): Sato, Y., Fukai, S.

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release